Sample-matrix preparation procedures are shown to greatly influence the quality of the matrix-assisted laser desorption/ionization (MALDI) mass spectra of peptides and proteins. In particular, dramatic mass discrimination effects are observed when using the matrix 4-hydroxy-?-cyanocinnamic acids for analyzing complex mixtures of peptides and proteins. The discrimination effects are found to be strongly dependent on the sample-matrix solution composition, pH, and the rates at which the sample-matrix co-crystals are grown. These findings demonstrate the need to exercise great care in performing and interpreting MALDI analysis of biological samples. The results also indicate that there is a chromatographic-like behavior in the sample-matrix preparation procedures that can be exploited to optimize the analysis. The present work describes the conditions under which the majority of components of a complex mixture of peptides and proteins can be successfully measured. A paper describing these results was published (S.L. Cohen and B.T. Chait, Anal. Chem. 68 (1996) 31-37.) We continue to investigate the influence of different sample preparation procedures on the information content in MALDI mass spectra and continue to make findings of practical importance